Zinc in PDB 6hsk: Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat

All present enzymatic activity of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat:
3.5.1.98;

The structure of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat, PDB code: 6hsk was solved by M.Marek, T.B.Shaik, E.Ramos-Morales, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.47 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	106.390, 106.390, 82.030, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 18.9

The structure of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat (pdb code 6hsk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat, PDB code: 6hsk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.5 occ:1.00 OD2 A:ASP267 2.0 31.9 1.0 OD1 A:ASP178 2.0 25.2 1.0 O4 A:GOK404 2.1 52.4 1.0 ND1 A:HIS180 2.2 33.7 1.0 O3 A:GOK404 2.3 36.8 1.0 N1 A:GOK404 2.8 50.9 1.0 C2 A:GOK404 2.8 39.2 1.0 CG A:ASP178 2.9 28.2 1.0 CE1 A:HIS180 3.0 32.2 1.0 CG A:ASP267 3.0 30.1 1.0 OD2 A:ASP178 3.1 28.4 1.0 CG A:HIS180 3.3 29.1 1.0 OD1 A:ASP267 3.4 29.0 1.0 CB A:HIS180 3.7 22.5 1.0 N A:HIS180 3.9 28.3 1.0 CA A:GLY304 4.1 33.2 1.0 C8 A:GOK404 4.2 35.4 1.0 NE2 A:HIS180 4.2 32.2 1.0 N A:LEU179 4.2 31.3 1.0 CB A:ASP178 4.3 24.2 1.0 CB A:ASP267 4.4 20.6 1.0 CD2 A:HIS180 4.4 27.4 1.0 NE2 A:HIS142 4.4 29.6 1.0 CA A:HIS180 4.4 30.4 1.0 N A:GLY304 4.5 39.7 1.0 CB A:LEU179 4.5 28.9 1.0 OH A:TYR306 4.6 38.1 1.0 C A:LEU179 4.7 32.0 1.0 CA A:LEU179 4.7 29.3 1.0 CE2 A:TYR306 4.8 27.8 1.0 C9 A:GOK404 4.8 28.9 1.0 CE1 A:HIS142 4.8 27.5 1.0 NE2 A:HIS143 4.9 29.2 1.0 C A:ASP178 5.0 30.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Human HDAC8 L6 Loop Mutant Complexed with Quisinostat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:41.3 occ:1.00 OD2 B:ASP267 2.1 32.2 1.0 OD1 B:ASP178 2.1 28.7 1.0 O4 B:GOK404 2.1 47.0 1.0 ND1 B:HIS180 2.2 31.0 1.0 O3 B:GOK404 2.3 38.8 1.0 N1 B:GOK404 2.8 49.5 1.0 C2 B:GOK404 2.9 44.7 1.0 CG B:ASP178 2.9 32.1 1.0 CG B:ASP267 3.0 31.7 1.0 CE1 B:HIS180 3.0 31.9 1.0 OD2 B:ASP178 3.1 25.5 1.0 CG B:HIS180 3.3 30.2 1.0 OD1 B:ASP267 3.3 30.8 1.0 CB B:HIS180 3.7 25.5 1.0 N B:HIS180 3.9 24.8 1.0 NE2 B:HIS180 4.2 29.5 1.0 CA B:GLY304 4.2 31.9 1.0 C8 B:GOK404 4.2 37.4 1.0 CB B:ASP178 4.3 22.0 1.0 N B:LEU179 4.3 25.7 1.0 CD2 B:HIS180 4.3 28.9 1.0 CB B:ASP267 4.4 28.7 1.0 CA B:HIS180 4.4 23.8 1.0 NE2 B:HIS142 4.4 31.8 1.0 N B:GLY304 4.5 31.3 1.0 O B:HOH646 4.5 51.8 1.0 CB B:LEU179 4.6 28.6 1.0 OH B:TYR306 4.6 39.2 1.0 C B:LEU179 4.7 33.3 1.0 CA B:LEU179 4.8 30.7 1.0 C9 B:GOK404 4.8 29.3 1.0 CE1 B:HIS142 4.8 32.9 1.0 CE2 B:TYR306 4.9 38.1 1.0 C B:ASP178 5.0 27.0 1.0 NE2 B:HIS143 5.0 31.0 1.0

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087